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Li R, Zhou L, Yang C, Xu WD, Huang AF. Relationship between SHP2 gene polymorphisms and systemic lupus erythematosus risk. Int J Rheum Dis 2023; 26:1485-1494. [PMID: 37270672 DOI: 10.1111/1756-185x.14761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/11/2023] [Accepted: 05/21/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disorder. SHP2, a non-transmembrane member of the protein tyrosine phosphatase (PTP) family, can be involved in multiple signaling pathways in inflammatory response. To date, it remains to be investigated whether polymorphisms in the SHP2 gene are correlated with SLE in the Chinese Han population. METHOD A study comprising 320 SLE patients and 400 healthy individuals was performed. Three single nucleotide polymorphisms (rs4767860, rs7132778, rs7953150) of the SHP2 gene were genotyped using the Kompetitive Allele-Specific Polymerase Chain Reaction method. RESULTS Genotypes of rs4767860 (AA, AG + AA) and rs7132778 (AA, AC + AA), and alleles of rs4767860 (A) and rs7132778 (A) were associated with SLE risk. Genotype AA of rs7132778 and allele A of rs7132778 and rs7953150 were associated with oral ulcers in SLE patients. Allele C of rs7132778 and genotype AA and allele A of rs7953150 were associated with pyuria. Patients who carried AA genotype and allele A of rs7953150 are more likely to develop hypocomplementemia. AA and AG genotype frequencies are more raised in patients with SLE with alopecia than in those without alopecia. Patients who carried AA and AG genotypes of rs4767860 had elevated C-reactive protein levels. CONCLUSION Gene polymorphisms of SHP2 (rs4767860, rs7132778) are relevant to SLE susceptibility.
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Affiliation(s)
- Rong Li
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Zhou
- Department of Preventive Medicine, School of Public Health, Southwest Medical University, Luzhou, Sichuan, China
| | - Chan Yang
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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Do DN, Schenkel FS, Miglior F, Zhao X, Ibeagha-Awemu EM. Genome wide association study identifies novel potential candidate genes for bovine milk cholesterol content. Sci Rep 2018; 8:13239. [PMID: 30185830 PMCID: PMC6125589 DOI: 10.1038/s41598-018-31427-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/14/2018] [Indexed: 12/31/2022] Open
Abstract
This study aimed to identify single nucleotide polymorphisms (SNPs) associated with milk cholesterol (CHL) content via a genome wide association study (GWAS). Milk CHL content was determined by gas chromatography and expressed as mg of CHL in 100 g of fat (CHL_fat) or in 100 mg of milk (CHL_milk). GWAS was performed with 1,183 cows and 40,196 SNPs using a univariate linear mixed model. Two and 20 SNPs were significantly associated with CHL_fat and CHL_milk, respectively. The important regions for CHL_fat and CHL_milk were at 41.9 Mb on chromosome (BTA) 17 and 1.6-3.2 Mb on BTA 14, respectively. DGAT1, PTPN1, INSIG1, HEXIM1, SDS, and HTR5A genes, also known to be associated with human plasma CHL phenotypes, were identified as potential candidate genes for bovine milk CHL. Additional new potential candidate genes for milk CHL were RXFP1, FAM198B, TMEM144, CXXC4, MAML2 and CDH13. Enrichment analyses suggested that identified candidate genes participated in cell-cell signaling processes and are key members in tight junction, focal adhesion, Notch signaling and glycerolipid metabolism pathways. Furthermore, identified transcription factors such as PPARD, LXR, and NOTCH1 might be important in the regulation of bovine milk CHL content. The expression of several positional candidate genes (such as DGAT1, INSIG1 and FAM198B) and their correlation with milk CHL content were further confirmed with RNA sequence data from mammary gland tissues. This is the first GWAS on bovine milk CHL. The identified markers and candidate genes need further validation in a larger cohort for use in the selection of cows with desired milk CHL content.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada
- Department of Animal Science, McGill University, Ste-Anne-de-, Bellevue, QC, H9X 3V9, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-de-, Bellevue, QC, H9X 3V9, Canada.
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada.
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Genetic Polymorphisms Associated with the Neutrophil⁻Lymphocyte Ratio and Their Clinical Implications for Metabolic Risk Factors. J Clin Med 2018; 7:jcm7080204. [PMID: 30096757 PMCID: PMC6111840 DOI: 10.3390/jcm7080204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Background: The neutrophil–lymphocyte ratio (NLR) is a valuable prognostic or predictive biomarker in various diseases, but the genetic factors that underlie the NLR have not been studied. We attempted to investigate polymorphisms related to NLR phenotype and analyze their ability to predict metabolic risks. Methods: A genome-wide association study was performed with log-transformed NLR using an Affymetrix Axiom™ KORV1.1-96 Array. Regression models for metabolic risk status were designed using the identified significant single-nucleotide polymorphisms (SNPs). Results: We identified four SNPs near the TMEM116, NAA25, and PTPN11 genes that were associated with the NLR. The top SNP associated with the log-transformed NLR was rs76181728 in TMEM116. A case–control study was performed to analyze the metabolic risks associated with each SNP after adjusting for age, sex, and body mass index (BMI). Three SNPs displayed significant odds ratios (ORs) for increased blood pressure and increased waist circumference. In the regression model for metabolic syndrome, rs76181728 showed a significant association (OR = 1.465, 95% confidence interval (CI) = 1.091–1.969, P = 0.011) after adjustment for the NLR phenotype. Conclusions: We identified four novel SNPs that are associated with the NLR in healthy Koreans. SNPs in relevant genes might therefore serve as biomarkers for metabolic risks.
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Coulombe G, Rivard N. New and Unexpected Biological Functions for the Src-Homology 2 Domain-Containing Phosphatase SHP-2 in the Gastrointestinal Tract. Cell Mol Gastroenterol Hepatol 2015; 2:11-21. [PMID: 28174704 PMCID: PMC4980741 DOI: 10.1016/j.jcmgh.2015.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/10/2015] [Indexed: 12/13/2022]
Abstract
SHP-2 is a tyrosine phosphatase expressed in most embryonic and adult tissues. SHP-2 regulates many cellular functions including growth, differentiation, migration, and survival. Genetic and biochemical evidence show that SHP-2 is required for rat sarcoma viral oncogene/extracellular signal-regulated kinases mitogen-activated protein kinase pathway activation by most tyrosine kinase receptors, as well as by G-protein-coupled and cytokine receptors. In addition, SHP-2 can regulate the Janus kinase/signal transducers and activators of transcription, nuclear factor-κB, phosphatidyl-inositol 3-kinase/Akt, RhoA, Hippo, and Wnt/β-catenin signaling pathways. Emerging evidence has shown that SHP-2 dysfunction represents a key factor in the pathogenesis of gastrointestinal diseases, in particular in chronic inflammation and cancer. Variations within the gene locus encoding SHP-2 have been associated with increased susceptibility to develop ulcerative colitis and gastric atrophy. Furthermore, mice with conditional deletion of SHP-2 in intestinal epithelial cells rapidly develop severe colitis. Similarly, hepatocyte-specific deletion of SHP-2 induces hepatic inflammation, resulting in regenerative hyperplasia and development of tumors in aged mice. However, the SHP-2 gene initially was suggested to be a proto-oncogene because activating mutations of this gene were found in pediatric leukemias and certain forms of liver and colon cancers. Moreover, SHP-2 expression is up-regulated in gastric and hepatocellular cancers. Notably, SHP-2 functions downstream of cytotoxin-associated antigen A (CagA), the major virulence factor of Helicobacter pylori, and is associated with increased risks of gastric cancer. Further compounding this complexity, most recent findings suggest that SHP-2 also coordinates carbohydrate, lipid, and bile acid synthesis in the liver and pancreas. This review aims to summarize current knowledge and recent data regarding the biological functions of SHP-2 in the gastrointestinal tract.
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Key Words
- CagA, cytotoxin-associated gene A
- ERK, extracellular signal-regulated kinases
- FGF, fibroblast growth factor
- GI, gastrointestinal
- HCC, hepatocellular carcinoma
- IBD, inflammatory bowel disease
- IEC, intestinal epithelial cell
- JMML, juvenile myelomonocytic leukemia
- KO, knockout
- MAPK, mitogen-activated protein kinase
- NF-κB, nuclear factor-κB
- PI3K, phosphatidyl-inositol 3-kinase
- PTP, protein tyrosine phosphatase
- PTPN11
- RAS, rat sarcoma viral oncogene
- epithelium
- gastrointestinal cancer
- inflammation
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Affiliation(s)
| | - Nathalie Rivard
- Correspondence Address correspondence to: Nathalie Rivard, PhD, 3201, Jean Mignault, Sherbrooke, Quebec, Canada, J1E4K8.3201Jean Mignault, SherbrookeQuebecCanada, J1E4K8
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SHP2 sails from physiology to pathology. Eur J Med Genet 2015; 58:509-25. [PMID: 26341048 DOI: 10.1016/j.ejmg.2015.08.005] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 02/08/2023]
Abstract
Over the two past decades, mutations of the PTPN11 gene, encoding the ubiquitous protein tyrosine phosphatase SHP2 (SH2 domain-containing tyrosine phosphatase 2), have been identified as the causal factor of several developmental diseases (Noonan syndrome (NS), Noonan syndrome with multiple lentigines (NS-ML), and metachondromatosis), and malignancies (juvenile myelomonocytic leukemia). SHP2 plays essential physiological functions in organism development and homeostasis maintenance by regulating fundamental intracellular signaling pathways in response to a wide range of growth factors and hormones, notably the pleiotropic Ras/Mitogen-Activated Protein Kinase (MAPK) and the Phosphoinositide-3 Kinase (PI3K)/AKT cascades. Analysis of the biochemical impacts of PTPN11 mutations first identified both loss-of-function and gain-of-function mutations, as well as more subtle defects, highlighting the major pathophysiological consequences of SHP2 dysregulation. Then, functional genetic studies provided insights into the molecular dysregulations that link SHP2 mutants to the development of specific traits of the diseases, paving the way for the design of specific therapies for affected patients. In this review, we first provide an overview of SHP2's structure and regulation, then describe its molecular roles, notably its functions in modulating the Ras/MAPK and PI3K/AKT signaling pathways, and its physiological roles in organism development and homeostasis. In the second part, we describe the different PTPN11 mutation-associated pathologies and their clinical manifestations, with particular focus on the biochemical and signaling outcomes of NS and NS-ML-associated mutations, and on the recent advances regarding the pathophysiology of these diseases.
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Han X, Zhang L, Zhang Z, Zhang Z, Wang J, Yang J, Niu J. Association between phosphatase related gene variants and coronary artery disease: case-control study and meta-analysis. Int J Mol Sci 2014; 15:14058-76. [PMID: 25123136 PMCID: PMC4159839 DOI: 10.3390/ijms150814058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 12/26/2022] Open
Abstract
Recent studies showed that the serum alkaline phosphatase is an independent predictor of the coronary artery disease (CAD). In this work, we aimed to summarize the association between three phosphatase related single nucleotide polymorphisms (rs12526453, rs11066301 and rs3828329) and the risk of CAD in Han Chinese. Our results showed that the rs3828329 of the ACP1 gene was closely related to the risk of CAD in Han Chinese (OR = 1.45, p = 0.0006). This significant association of rs3828329 with CAD was only found in the females (Additive model: OR = 1.80, p = 0.001; dominant model: OR = 1.69, p = 0.03; recessive model: OR = 1.96, p = 0.0008). Moreover, rs3828329 was likely to exert its effect in females aged 65 years and older (OR = 2.27, p = 0.001). Further meta-analyses showed that the rs12526453 of PHACTR11 gene (OR = 1.14, p < 0.0001, random-effect method) and the rs11066301 of PTPN11 gene (OR = 1.15, p < 0.0001, fixed-effects method) were associated with CAD risk in multiple populations. Our results showed that the polymorphisms rs12526453 and rs11066301 are significantly associated with the CAD risk in multiple populations. The rs3828329 of ACP1 gene is also a risk factor of CAD in Han Chinese females aged 65 years and older.
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Affiliation(s)
- Xia Han
- Department of Cardiology, Laiwu People's Hospital, Laiwu 271100, China.
| | - Lijun Zhang
- Department of Cardiology, Laiwu People's Hospital, Laiwu 271100, China.
| | - Zhiqiang Zhang
- Department of Cardiology, Laiwu People's Hospital, Laiwu 271100, China.
| | - Zengtang Zhang
- Department of Cardiology, Laiwu People's Hospital, Laiwu 271100, China.
| | - Jianchun Wang
- Department of Cardiology, Shandong Provincial Hospital, Jinan 250000, China.
| | - Jun Yang
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China.
| | - Jiamin Niu
- Department of Cardiology, Laiwu People's Hospital, Laiwu 271100, China.
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